Instead of FASTQs, users can provide their own BAM files as input to the pipeline. However, the current behavior still calls samtools to remove duplicates from the BAM files (and MACS2 to call peaks from them).
I could have it skip the duplicate removal steps if a BAM file is provided, instead. And I could have it skip the peak calling step if a BED file is provided with the BAM file.
Instead of FASTQs, users can provide their own BAM files as input to the pipeline. However, the current behavior still calls samtools to remove duplicates from the BAM files (and MACS2 to call peaks from them).
I could have it skip the duplicate removal steps if a BAM file is provided, instead. And I could have it skip the peak calling step if a BED file is provided with the BAM file.